INDRA documentation

INDRA (the Integrated Network and Dynamical Reasoning Assembler) assembles information about biochemical mechanisms into a common format that can be used to build several different kinds of explanatory models. Sources of mechanistic information include pathway databases, natural language descriptions of mechanisms by human curators, and findings extracted from the literature by text mining. Mechanistic information from multiple sources is de-duplicated, standardized and assembled into sets of mechanistic Statements with associated evidence. Sets of Statements can then be used to assemble both executable rule-based models (using PySB) and a variety of different types of network models.

License and funding

INDRA is made available under the 2-clause BSD license. Users are asked to acknowledge DARPA grant W911NF-14-1-0397, “Programmatic modelling for reasoning across complex mechanisms,” Peter Sorger and Dexter Pratt PIs.


Indices and tables